How to make deposition of images a reality

Guss, J. Mitchell; McMahon, Brian

doi:10.1107/s1399004714005185

Cited by 21 publications

(18 citation statements)

References 24 publications

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“…Nature, Science, Structure, Protein Science, etc. ).Deposition of experimental raw data by research groups should become a standard and should be performed via established repositories capable of assigning digital object identifiers (doi) (Guss and McMahon, 2014). These repositories may either be established as part of the PDB itself or via the journal initiatives described above.…”

Section: Conclusion and Recommendationsmentioning

confidence: 99%

Safeguarding Structural Data Repositories against Bad Apples

et al. 2016

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Structural biology research generates large amounts of data, some deposited in public databases/repositories, but a substantial remainder never becoming available to the scientific community. Additionally, some of the deposited data contain less or more serious errors that may bias the results of data mining. Thorough analysis and discussion of these problems is needed in order to ameliorate this situation. This note is an attempt to propose some solutions and encourage both further discussion and action on the part of the relevant organizations, in particular the Protein Data Bank and various bodies of the International Union of Crystallography.

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Section: Conclusion and Recommendationsmentioning

confidence: 99%

Safeguarding Structural Data Repositories against Bad Apples

et al. 2016

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“…In a recent paper, Guss & McMahon (2014) formulated eight essential attributes of an 'Image Archive', representing an ideal entity managing the storage of protein diffraction images for the crystallographic community. These are the following.…”

Section: Discussionmentioning

confidence: 99%

“…The potential benefits of archiving raw diffraction-image data (Terwilliger & Bricogne, 2014;Terwilliger, 2014;Meyer et al, 2014;Kroon-Batenburg & Helliwell, 2014;Guss & McMahon, 2014) include the opportunity to improve existing PDB depositions, the provision of training and test sets for methods development, and the prevention of loss of data upon the closure of laboratories and collaborative programs.…”

Section: Introductionmentioning

confidence: 99%

A public database of macromolecular diffraction experiments

Grabowski

Langner

Cymborowski

et al. 2016

Acta Crystallogr D Struct Biol

109

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The low reproducibility of published experimental results in many scientific disciplines has recently garnered negative attention in scientific journals and the general media. Public transparency, including the availability of `raw' experimental data, will help to address growing concerns regarding scientific integrity. Macromolecular X-ray crystallography has led the way in requiring the public dissemination of atomic coordinates and a wealth of experimental data, making the field one of the most reproducible in the biological sciences. However, there remains no mandate for public disclosure of the original diffraction data. The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) has been developed to archive raw data from diffraction experiments and, equally importantly, to provide related metadata. Currently, the database of our resource contains data from 2920 macromolecular diffraction experiments (5767 data sets), accounting for around 3% of all depositions in the Protein Data Bank (PDB), with their corresponding partially curated metadata. IRRMC utilizes distributed storage implemented using a federated architecture of many independent storage servers, which provides both scalability and sustainability. The resource, which is accessibleviathe web portal at http://www.proteindiffraction.org, can be searched using various criteria. All data are available for unrestricted access and download. The resource serves as a proof of concept and demonstrates the feasibility of archiving raw diffraction data and associated metadata from X-ray crystallographic studies of biological macromolecules. The goal is to expand this resource and include data sets that failed to yield X-ray structures in order to facilitate collaborative efforts that will improve protein structure-determination methods and to ensure the availability of `orphan' data left behind for various reasons by individual investigators and/or extinct structural genomics projects.

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“…The deposition and the wide availability of raw diffraction data have far-reaching benefits for the structural biology community (Joosten & Vriend, 2007;Jones & Kleywegt, 2007;Androulakis et al, 2008;Guss & McMahon, 2014). We recently created TARDIS, a suite of tools for the deposition of X-ray diffraction images in an open-access repository to facilitate their deposition using federated institutional repositories (Androulakis et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

Operation of the Australian Store.Synchrotron for macromolecular crystallography

Meyer

Aragão

Mudie

et al. 2014

Acta Cryst D Biol Crystallogr

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The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The service automatically receives and archives raw diffraction data, related metadata and preliminary results of automated data-processing workflows. Data are able to be shared with collaborators and opened to the public. In the nine months since its deployment in August 2013, the service has handled over 22.4 TB of raw data (∼1.7 million diffraction images). Several real examples from the Australian crystallographic community are described that illustrate the advantages of the approach, which include real-time online data access and fully redundant, secure storage. Discoveries in biological sciences increasingly require multidisciplinary approaches. With this in mind, Store.Synchrotron has been developed as a component within a greater service that can combine data from other instruments at the Australian Synchrotron, as well as instruments at the Australian neutron source ANSTO. It is therefore envisaged that this will serve as a model implementation of raw data archiving and dissemination within the structural biology research community.

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How to make deposition of images a reality

Cited by 21 publications

References 24 publications

Safeguarding Structural Data Repositories against Bad Apples

Safeguarding Structural Data Repositories against Bad Apples

A public database of macromolecular diffraction experiments

Operation of the Australian Store.Synchrotron for macromolecular crystallography

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